The Matrix: The New Prophecy
by kmylove
Summary: What if things aren't what they seem to be? 25 years after Neo's final battle with Smith a new prophecy announces the end of the war... FINAL CHAPTER UPLOADED REVIEWS are welcome. Credits to x.ShatteredImage.x for her contributing her great ideas
1. 1 Cause and Effect

_**CHAPTER 1: CAUSE AND EFFECT...**_

_The action of this first chapter takes place some months after Neo's last battle with Agent Smith..._

A very dark night on the streets of the Matrix...even darker than it was usually made by the machines... The deep silence of the night was suddenly disturbed by rushed footsteps... A dark silhouette rushed through the streets, keeping close to the walls... The black cloak covered the person from head to toes...

The mysterious stranger stopped in front of a small building in the fictive China Town... It stopped a while to catch its breath... It took a quick glance behind to be sure that it was safe... A knock on the door...

"What are you doing here?" Seraph asked at opening the door.

"I must see her!" a soft woman's voice answered... "I must get in, please Seraph!"

"You know you are forbidden to be here! Leave or suffer the consequences!" seraph raised his voice and took a threathnig position...

"Suffer the consequences...funny...I already am suffering the consequences of my deeds", the woman muttered as a tear ran down her cheek...

"What are you talking about, woman? Leave at once!"

"Seraph, let her in!" said the Oracle coming from behind him. "It's safe, I know that. And it really is important. Come in!"

The woman followed the Oracle inside the house.

"Thank you for letting me in, mother! You know this is the last time we meet... I've come to give you my baby" the woman said, revealing the baby that she held under the cloak, "I know you are the best person to take care of it, to protect it from what may come..."

"Oh, my child, why did you do such a thing?"

"You will never understand! I just had to!" the woman said, bursting into tears. "I've always hated this gift that I've inherited from you...seeing the future, knowing Fate...it's awful! And now this gift has become my curse! Cause and effect, I guess... I knew what to do to end this stupid war between man and machines and I did it... Now, as soon as I walk out that door my life will end..."

"My child, you always knew you mustn't interfere with the future!"

"But I just had to! I knew one sacrifice wouldn't be enough to save the world! I did it because I loved him more than anyone could possibly understand!"

"How cruel life is, my daughter... Love has taken you away from me once, and now love will make me loose you again", said the Oracle.

"Please, he's almost here! I must leave or else I will put you into danger... Take my baby... I know you know just what to do so that the Prophecy fulfills at its due time... Farewell, my child! Farewell, mother!" said the woman putting the baby into the Oracle's arms.

"Farewell!"

The woman in black walked out the door.

Seraph came into the room. The Oracle was crying with the baby in her arms. In so many years he had never seen her cry...

"Oracle, I have never seen you cry!"

"If you could see what awaits this poor soul, you would cry too...all the pain, all the sufferance... All of this for a noble cause, for PEACE!" The Oracle wiped her tears. "Seraph, let's take the baby to a safe place..."

The woman ran out of the Oracle's house crying like she never did before in her life...But she stopped after a short distance, realizing that nobody was following her...That was not right, it was not as she had seen it would be... Images rushed through her mind so quickly that she couldn't understand anything... She knew something had changed, but she kept running until she entered a park. Exhausted she sat down on a bench... She kept trying to have a clear image of what will happen when she felt the cold steel of a gun on her neck... So nothing changed, after all...

"Just this once be a gentleman and don't shoot me at the back", she whispered, trying to be brave. She turned around. The night was so dark that she couldn't see the face of her assassin. She took her black cloak off and let it fall on the ground... She gently grabbed the gun and pointed it to her chest...

"At least be a man and show yourself, my darling. Look me in the eyes when you do it!"

The man took one step forward, pressing the gun into her chest. She still couldn't see his face but she caught a glimpse of his eyes... She was shocked, that couldn't be happening! She tried to say something, but it was too late. The gunshot echoed throughout the park. Another sacrifice was made in the name of peace...


	2. 2 Time Goes By

_**CHAPTER 2: TIME GOES BY...**_

Many things have happened in 25 years...

Peace proved to be fragile, it only lasted for one year… But it was a great year. Everyone was free to leave the Matrix whenever they wanted. Even the free people of Zion were free to get back in if they wanted. The machines changed the Power Plant. Instead of the cocoons, now people would lie on beds and have a helmet on their head, which controlled their brain waves. Getting out was more easy too, they just had to take the red pill and they woke up. Zion became a prosperous city. The Agents were all destroyed, as well as many programs.

Everything was ruined the night when Morpheus got shot by the Phantom. Since Neo and Trinity's death he had been trying hard to recover their bodies from Machine City. He wanted them back to Zion, because they were the heroes of the city. In his actions he did many things that seriously endangered the fragile peace. Yet, one dark night, in a dark alley, he got shot at the back by a man wearing a white mask. Before dying he managed to pull the mask of his face. The shock was great but he didn't get to say anything.

Niobe was devastated by his death. He was pregnant and some months later she gave birth to two twins: Castor and Pollux, two boys that would grow to look exactly like their father.

Morpheus' death meant the end of peace. Zion and the Machines were back at war. No person was allowed to jack out any more. Many people found themselves prisoners back in the artificial world. The citizens of Zion were outcasts again. Getting people out of the Matrix became an ordeal. The agents were brought back, but none of them was such a great menace as the Phantom was. The Phantom, the same man who had shot Morpheus, would kill everyone that tried to get out and everyone that would try to get them out. Many brave soldiers of Zion died in mission, killed by him. He never missed a target. He was Zion's number one enemy.

Castor and Pollux became soldiers, although Niobe disagreed. They had studied every piece of archive that they could find related to their father, to Neo and Trinity…They took charge of the Neb and tried to free many people, like their father did, years ago... And like their father, they had a prophecy to believe in…

In the 25 th year the Oracle made a new prophecy. All those changes did not affect her in any way. She and Seraph never changed, in any way. Now, she predicted that in less the one year's time the war would be over. Castor and Pollux received the mission to continue saving people and find The Chosen One. That was all she said…to look for The One. Not another detail…


	3. 3 Shadows Of The Night

_**CHAPTER 3: SHADOWS OF THE NIGHT**_

A quiet night… Midnight… The young lady was sleeping peacefully, maybe one of the few nights when she had a peaceful sleep. Suddenly she felt something cold on her forehead an opened her eyes… The Phantom was pointing a gun at her head and shot…

She jumped out of bed looking at the clock… Five minutes to midnight and she was all alone in the room, but she knew it was not a dream that she had and that she must hurry. She ran to the fire escape but instead of going down in the street, she went up to the rooftop. She couldn't explain what was happening to her… Two years ago she woke up in a hospital, without any memory of her past. They told her it was a miracle that she was the only survivor of such a dreadful accident, but she had no idea what they were talking about… She kept trying to remember but all she could get into her mind were fragments of images that made no sense…

Her life was very complicated since then. For some reason it seemed that everyone wanted to kill her since she woke up. If she was still alive by now it was because for some strange reason she could foresee what will happen to her and she could get away before getting hurt… She found she could do some amazing things, but now she had no time to remember all this, she had to run for her life, as she knew it was hard to escape alive from a meeting with the Phantom.

She ran hard towards the edge of the rooftop and closed her eyes while taking a giant leap to the neighboring one. At landing she stopped to look back.

"How on earth did I do that?" she wondered. She saw the silhouette of the Phantom approaching the edge. She continued running, jumping more and more rooftops, then taking a jump down and into the park.

She stopped a while to draw her breath… Someone touched her on the shoulder… she wanted to scream…

"Don't scream, he'll hear you!"

"Castor, you've scared me" she said.

"What? How did you know my name? Who are you?" Castor asked, very surprised that the girl he wanted to save that night knew him by the name…

"How did I know your name? Good question… I just did… You look so familiar…" she said, then she suddenly pushed Castor away from her telling him to run for his life…

Castor listened to her and he ran. Behind he heard a gunshot. He stopped to look back and saw the girl fall, she had been shot in the stomach… He was surprised to see that the Phantom wouldn't chase him, and just went away… Castor continued his run to get his brother Pollux there to help him figure out what had happened.

When they returned, they found the girl laying down, with her hands on the wound. There was no blood around. They removed her hands and were shocked to see that the wound was healed. They felt her pulse… she was alive, she was just sleeping.

Castor and Pollux decided that they should get her out of the Matrix that night… They felt that they might have accomplished their mission. The twins brought the car round and put the girl on the back seat. They drove away to the hotel, the old hotel, to the safest place they knew, to the gate for their way home… They were anxious that she woke up so she could answer all their questions…


	4. 4 Phoenix

_**CHAPTER 4: PHOENIX**_

Castor and Pollux were looking at the young woman they had in front of them, tormented by many questions. They were fascinated by her long black hair and her amazingly divine face features. They waited for her to wake up, because she would have a lot of explaining to do…

They had already called Operator to trace her signal so they could get her out if it turned out she was good. Link was not in charge of the communications any more, he quit after Morpheus died. Now in charge was a young smart man called Cryptex.

Finally she opened her brown deep eyes. On seeing them, she got scared and wanted to run away, but Pollux pointed the gun at her head:

"Stop right there! You have some questions to answer! And you're leaving until you do it!"

"OK, whatever… Just get that gun away from me, you're playing with fire, Pollux!"

"What? How do you know my name?"

"Haven't I told you that she knew mine, dear brother?" Castor answered.

"Hush, Castor! Now: who are you? And…WHAT are you?" Pollux made his first question.

"What am I? Really now, what do I look like? Or should I presume that you haven't seen a woman before? As for who am I… that's going to be hard to answer as I don't know myself…"

"That's ridiculous! Stop mocking us and answer! Who are you?", Pollux asked pointing the gun at her again.

"Funny thing, although you are pointing a gun at my head, I know I can trust you, because I see you are afraid of firing a gun at me. So, to begin my story… I woke up about two years ago on a hospital bed, and I could only remember one thing: that my name is Phoenix. Nothing else besides that. They told me I was the only survivor of a horrible accident, but I can't remember anything at all. All I have are some images that don't make any sense at all. Instead, I seem to be able to know other people's past and future and even their thoughts…" she sighed

"I think we both had a taste of that, didn't we Pollux?" Castor laughed.

"Could you be serious, Castor? Phoenix, you say that everyone keeps wanting to kill you? You certainly don't mean The Phantom! No one has ever escaped him!"

"Well, I'm sorry to disappoint you, but I do mean him! At first I was hunted by the Agents, but I always predicted their attacks and they couldn't harm me at all… Then came the Phantom himself. With him it's always hard to escape. Thanks to him I discovered I could do some very unusual things… I found myself jumping off rooftops and all sorts of things no one can do…"

"Would one of them be what I saw tonight?" Castor asked.

"I don't know what you saw!" Phoenix answered.

"I saw him shoot you, I saw you were injured, then we found you safe and sound sleeping!"

"Oh, that… The first time me and the Phantom met, he shot me in the chest. As an instinct I putt my hands above the wound and after a while I fainted. When I woke up…the wound was gone…

It was like that that I've discovered could heal myself of any wound, and apparently other people too…"

"I have a curiosity! You've said you've met the Phantom more than once… Being that you can read minds and all, do you know who he is? We're after him for a long while!" Pollux asked.

"I did read his mind…just once…if you could do it just for a few seconds, you'd wish you never do it again! He only thinks of one thing: revenge! He is very angry and determined to kill…"

Castor's cell phone rang. It was Cryptex:

"Castor, we've traced her, you might want to hear this: she is not connected through the Power Plant. She is in Machine City!"

"What? And how can we get her out?"

"Curiously, the Sentinels deactivated themselves when we approached the place. Almost as if they want us to get her out! Should we proceed?"

"Yes, proceed, we're almost done…"

Phoenix looked at him a little puzzled. She knew what they spoke of.

"Look, Phoenix, we know you're confused because of your situation, but there's more you need to know…" Castor spoke.

"About the Matrix, you mean? I know everything, I've figured it out by myself that this is not the real world we live in. I knew you would come to take me out… I know what you'll do next, you'll take out a red pill and you'll tell me it will get me out. And I feel that taking the red pill will be the worst thing that I ever did and that it will make me suffer, but I also know it will have good consequences…" Phoenix sighed.

Castor gave her the red pill and she took it. Tears were running down her face. She could see millions of things that made no sense but that made her suffer. She close her eyes and swallowed the pill.

At opening them she was lying on a metal bed surrounded by Castor, Pollux and some people she had never seen before…

TBC


	5. 5 Reality Bites

_**CHAPTER 5: REALITY BITES**_

Castor was the first one to speak:

"Good morning, sleeping beauty! We thought we lost you!"

"What happened? Why do you say that?" Phoenix asked, looking around her surprised.

"You've been asleep for three days and there was no way we could wake you up" Pollux answered. "Are you OK?"

"Yes, I am. I guess I was too exhausted after all that happened, with the Phantom and with leaving the Matrix… I'm so confused right now…"

"We'll tell you everything there is to know. First let us introduce you to our mother, Niobe" Castor spoke.

Phoenix looked at Niobe, a woman that looked older than she should be and she felt all of her pain. Just by looking at her eyes she saw the whole story of her and Morpheus and she felt the wish for revenge that she had against the Phantom.

Then they introduced her to the rest of the crew on the Neb.

"Now we'll leave you with Cryptex. He'll show you everything there is to know." Castor said.

Cryptex told Phoenix everything about The Matrix, in detail. The part which he was most interested in was explaining to her about The One. Cryptex showed her images of Neo and the amazing things he had done in the Matrix. But while seeing the images of him fighting agents, she could see his whole life, she could see him and Trinity, she could feel their love story and she burst into tears at seeing them die. But there was one thing she couldn't see, as hard as she tried: she couldn't see what happened to them after their death.

The first thing was a little hard for Phoenix, she had to accommodate to a different lifestyle, a harsh one…

One day, Castor and Pollux decided that it was time to see if Phoenix was right when she said that she could to things no one could.

"We'll get you into a training program. You'll have to fight some agents. We want to see what you can do" they said to her.

"Really? You're doing this because you hope I am The One, right? Even I don't know if your hopes will come true. But now let me amaze you" Phoenix answered in her ironic style.

She laid on a bed and Cryptex put the helmet on her head. In a matter of seconds she was in the program, which simulated the rooftop of a very tall building. She was wearing a scarf around her eyes.

"Phoenix, do you hear me? Take that scarf off!" Pollux spoke.

"I hear you Pollux, but I won't please you! You wanted me to surprise you, right? So here I go…"

Agents came up. Although she had her eyes covered, she fought each one of them in a perfect way. None of them even got a chance to hurt her. She could see in her mind from where she will be attacked so she could react before anything happened.

The twins and Cryptex were amazed. Cryptex was ordered to let in armed agents and so he did.

They were stunned to see that Phoenix could dodge all the bullets. They hadn't seen anyone move like that! Not even in the old recordings of Neo! She was amazing. All they could think was that Phoenix must be The One, that the young woman that didn't have a past will save the future.

"Enough" Pollux said.

Phoenix took off the scarf, with an ironic smile.

"Great job! Let's get you…" but Pollux didn't get a chance to finish his sentence because at looking on the monitor he saw behind Phoenix none other than the Phantom. He was standing just a few inches away from her. Pollux was as shocked to see that she wouldn't react in any way as he was by the fact that Phantom managed to break into their safe system.

"Phoenix, run! Why are you standing there?" Castor screamed into the microphone. But she didn't seem to hear him.

She started moving slowly towards the edge of the rooftop, with her eyes closed. Cryptex was trying hard to get her out, but the program would not respond.

Phoenix stood for a few seconds on the edge, then she jumped. She was falling fast and no one could do anything to get her out in time. Just a few inches before reaching the ground she opened her eyes and made such a sudden stop that all the windows off the building shattered into millions of pieces.

Cryptex finally got her out. At waking up she began crying. Castor rushed to hug her.

"What happened? Why did you just stay there?" Pollux asked.

"I don't know. I felt the Phantom coming and I wanted to turn around and shoot him but I couldn't. He told me that he would get rid of me to complete his revenge and he told me to jump off the building. I tried not to listen to him but I couldn't… He was in my mind, he controlled me. I managed to fight his will and when I opened my eyes I got so scared at seeing that I almost hit the ground! I'm so afraid of him! I never imagined he could do that!" she said and burst into tears again.

Castor, Pollux and Cryptex looked at one another, not knowing what to do to console her. They were trying to understand how their worst enemy got there.

TBC


	6. 6 Out Of The Darkness

_**CHAPTER 6: OUT OF THE DARKNESS**_

Phoenix stood alone in her room for many days, crying and trying to understand what had happened, why was she so close to dying in such an odd way. She didn't want to get back into the Matrix and she feared to meet the Phantom again. She thought she deserved what was coming to her, because she was too proud and she believed she could defeat the Phantom.

"Phoenix, the Oracle wants to see you. We have to go" Castor told her one day after coming into her room.

"Does this mean I have to go back in… I'm still afraid, I have a bad feeling about this" Phoenix answered.

Castor gave her an embrace. She leaned her head upon his chest, sobbing.

"Don't worry, I'll protect you, no matter what…" he said grabbing her by the chin and looking into her beautiful eyes. Their lips touched. Castor gave Phoenix the first kiss she had in her life… A kiss which made her understand that he had fallen in love with her before meeting her in the park, she realized that he had been following her for a long time, that them meeting that night was not a coincidence. But she also saw their future, he saw him suffering because of her… She broke free from his arms

"No, Castor! Don't, please! I don't want to hurt you… I…love…you…and I don't want you to suffer" Phoenix explained.

"I won't suffer! Let me love you!"

Phoenix didn't say a word. She headed for the door.

"Let's go to the Oracle…"

The Oracle first wanted to see the twins. She told them that their mission was over and asked them to let Phoenix in.

At seeing the Oracle Phoenix suddenly remembered a piece of her past:

"I remember you…before waking up…I saw you…you told me that…it was time to wake up and fulfill…my destiny… Who are you? What do you know about me?"

"You remembered this because I wanted you to remember. I know everything about you!"

"Please, tell me what you know!" Phoenix answered.

"I can't tell you everything now, but I can show you something…"

After the Oracle said this, Phoenix closed her eyes. She could see a woman dresses in black, giving a baby to the Oracle, then running in the park and being shot by the Phantom.

She opened her eyes.

"Am I the baby? Is she my mother? Why did he shoot her?"

"All I can tell you is that you are the baby. To find out more, you must go to Machine City." The Oracle answered.

"Machine City? That was where they found me… What will I find there?" Phoenix asked, confused because she could not see what waited for her there.

"Don't try to see what I'm not letting you see! You'll find pieces of your past, that will influence the future. Now go and do what you must do! I'll call you again at the right moment".

"Before I go, I must ask you something… Castor, Pollux, everyone in Zion, they think I am The One and I will end the war…but I don't know how…"

"For now you should only know this: to end the war you must destroy what caused it…"

"From what they told me, the war burst back after Phantom killed Morpheus… so I must kill The Phantom? But I am afraid of him…"

"You will know more after you come back from Machine City"

Phoenix left. She told Castor that they should go back to Zion and let her take The Neb to Machine City. He wanted to go with her, but she refused, saying it was something she must do by herself, no matter how dangerous it was. Finally he agreed.

TBC


	7. 7 Return To Inocence

_The giant robotic head to whom Neo talks in the Revolutions is credited as The Deus Ex Machina, so I'll use this name to refer to him in this chapter._

_**CHAPTER 7: RETURN TO INOCENCE**_

Phoenix was surprised to see that all the sentinels were deactivating themselves as she passed them by in the Neb. This made her remember that Castor and Pollux told her that in the night when they took her out of the Matrix the Sentinels were also mysteriously deactivated.

She closed her eyes for a moment…she recalled the moment when Neo and Trinity's ship crashed…

Neb landed in Machine City. Phoenix stepped out, looking around her…she could see back 25 years ago…Neo finding his way through the darkness…

She stopped. A huge robot appeared in front of her and spoke:

"I've been expecting you Phoenix"

"How did you know I was coming?" she asked.

"She told me" the Deus Ex Machina answered.

"She? She who?" asked Phoenix, thinking that it could have been the Oracle.

"I can't answer that! You came to take what belongs to you and Zion and I'll give it to you!"

"But why would you help me and Zion? Helping us will destroy you" Phoenix said, fearing she might have been caught in a trap.

"I'm not helping you at all! I'm just making things more complicated! Follow the Sentinel!"

Phoenix looked behind her and saw a sentinel. She decided to follow, although she feared the huge metal structure of the Sentinel. It brought to her mind so many images about the war.

The Sentinel stopped in front of two bed-like structures.

Phoenix was paralyzed by what she saw…that couldn't be! How could it be?

In front of her laid Neo and Trinity, looking as young as they were 25 years ago! What's more, trinity had no wound and Neo's eyes were healed too. How could it be?

The Sentinel grabbed them with its tentacles and started heading slowly for the Neb. Phoenix followed, trying to figure out why were the two heroes of Zion there and why did the Oracle tell her that she would find pieces of her past…did that mean that they were pieces of her past? How?

The Sentinel put the two bodies into the Neb and left. Phoenix placed them on the two beds they used to get into the Matrix and took her place in the pilot seat. She took off calling Cryptex:

"Cryptex, I'm heading back for Zion! Tell Castor and Pollux to come to the docks as soon as I land, tell them to get ready to board the Neb again… And tell them to bring Niobe…and Link…

It's very important!

Castor, Pollux, Niobe and Link boarded the Neb. Castor rushed to hug Phoenix, happy to see that she was OK.

"Did you find out why the Oracle sent you to Machine City?" Castor asked.

"I did…you're not going to believe this…I couldn't myself. Follow me!" Phoenix answered, leading their way to the control room.

Niobe and Link were speechless at the sight. Neo and Trinity! Finally they were HOME!

"They appear to be in a coma… That's why I called you Link. You know better. See what's with them" Phoenix spoke.

Link put a helmet on their head and begun scanning their brain waves and scanning the Matrix. After about ten minutes he spoke:

"Trinity is fine, she's just in a coma, we need to wake her up. But Neo… it's weird… This happened to him before… He has some activity but does not appear to be in… I don't think we can wake him up"

Castor was contacted by Cryptex.

"The Oracle called. She wants to see Phoenix and Trinity tomorrow. She said that Phoenix will know how to wake her up…" Castor told everyone.

Phoenix stood a moment looking at Trinity… she took her hand and concentrated… She closed her eyes…

Everyone waited to see what will happen.

In a matter of minutes Trinity took a deep breath and opened her eyes. Phoenix collapsed, exhausted. Castor rushed to help her.

Trinity looked around her very confused…

"Neo! Where is Neo?" she asked, remembering the crash that their ship took.

"Trinity, old friend!" Niobe said, taking her hand "there are many things you must know"

TBC


	8. 8 Truth Hurts

_**CHAPTER 8: TRUTH HURTS**_

Trinity couldn't sleep that night… So many question he needed the answer to… Niobe told her what happened during her 25 year absence, but still… how could it be? How could she be alive? How come she didn't age? She should be 55 years old… And the war was not over? Morpheus dead? And The Phantom being a threat to everyone? She couldn't wait to visit the Oracle, she knew she would give her all the answers…

Phoenix was exhausted after waking Trinity up. She barely had any pulse when Castor took her into bed. He was so worried that he stood by her side all night.

She woke up late the next day, just when the Oracle communicated with them and announced she would receive Trinity and Phoenix.

"Welcome, Trinity! Nice to see you again!" the Oracle said as the two walked trough the door.

"Oracle, please, tell me what happened! I have so many questions!" Trinity spoke.

Phoenix didn't say a thing. She had many questions to ask too, but she knew it was more important for Trinity to be answered.

"I know you have, dear! And I know you have many questions too, Phoenix. Have a seat and I'll tell you the entire story…"

"What happened to me and Neo?" Trinity asked.

"You and Neo were saved by my…daughter"

"Your daughter?" Trinity asked stunned "You have a daughter?"

"I HAD a daughter. She was a very rebel child, she never liked the fact that she could see the future, read thoughts, she never liked her powers… When she grew up she fell in love and left me. I guess she loved that The Merovingian hated me…"

"The Merovingian? You mean to tell us that your daughter was…PERSEPHONE?" Trinity was more surprised than before. "And you say that she saved us? That SHE saved ME?"

"Yes, Trinity! You see, when you first went with Neo and Morpheus at the Merovingian's castle, to find the Keymaker, Persephone saw the future that you two had, she knew that you were both destined to die. And she also saw another thing, something that neither you nor Neo knew at the moment. That something was the salvation of you two and of the world… And because she had fallen in love with Neo, she decided to help him at any cost… and the cost was to be high…"

"But… what did she see?" Trinity asked, jealous of Persephone.

"Trinity, Persephone saw that you were pregnant! You were to have a child!" the Oracle revealed.

Trinity couldn't believe what she was hearing. She, a mother?

Phoenix suddenly began to realize that Trinity's story might indeed concern her, more than she imagined.

"What happened to the child?" Trinity could barely ask.

"I'll explain immediately… After your ship crashed and you died, Persephone, who had followed you, came and took you to Machine City. She used her powers to bring you back to life and healed your wounds, but she kept you in a come until you gave birth. After that she had the machines keep you in a cryogenic state, knowing that one day you will be brought back. She was the one to heal Neo's eyes and he was kept in cryogenic state too, except that his situation was worse…"

"But you say I gave birth! Where is my baby?" Trinity asked.

Phoenix looked at her and she realized everything that the Oracle was going to say… she could see everything that happened. She closed her eyes and continued:

"Persephone decided to take your baby. But her husband found out what she did and decided it was time that she paid for helping his worst enemy. He went after her to kill her. She knew she would die. So she decided to get the baby in a safe place. She put on a black cloak and came to the Oracle's house. Before handing her the baby, she gave her powers to it, she knew it would need them to save the world. Then she left knowing that she would be shot by the Merovingian as she walks out the door. But that didn't happen. She couldn't see any more, she couldn't see that her husband had been shot by the Phantom while following her… that the Phantom would kill her in the park…" Phoenix burst into tears "That's my story, I WAS THE BABY!"

Trinity was stunned… that young girl was her daughter? Neo's daughter? She waited for the Oracle to give her details.

The Oracle spoke:

"That is right, Phoenix! Trinity and Neo are your parents!

Trinity and Phoenix stared at each other, speechless, crying for minutes… Then they gave each other a warm embrace.

Phoenix had more questions for the Oracle:

"Why can't I remember my past? What did you do with me after Persephone left me here?"  
"I knew it wasn't safe to keep with me. I took you to Machine City. I had the Architect make you your own reality, your own world, a world where I had him connect Trinity too, while she was in her coma. You two lived there like mother and daughter, until it was time to get you Phoenix out to do what you had to do: saving the world…"

"You say you connected me…what about Neo? Why didn't you connect him too?" Trinity asked.

"Neo…I'm afraid things are not that easy with Neo. He was severely affected by his last battle with Smith…"

"What happened to him? After all, he is still alive!" Trinity insisted.

"I'm afraid I can't tell you more right now. You'll find out everything at the right time" the Oracle answered.

"Oracle, tell me, how will I defeat the Phantom? How will Trinity help me?" Phoenix asked.

"You will know soon. Just give it a little time. Now you should go back."

"See you soon, Oracle" Trinity said at walking out the door.

"Sooner than you think, Trinity…" the Oracle said to herself.

Phoenix and Trinity were too shocked by what they found out to speak. Phoenix was lost in her thoughts, confused by everything, that she didn't even pay attention to where she was walking. Trinity was also very confused. She just walked behind Phoenix. She paid attention to Phoenix only when she noticed she had stopped.

They were in the park, the same park where Persephone had been killed.

They looked at each other. They had so many things they wished to say, but neither of them had the courage to say anything.

Back on the Neb, everyone was waiting for their return, following them on the monitors, wondering why were they so quiet, what did the Oracle tell them. They saw them stop in the park and look at each other quietly.

Then they heard a gunshot and the monitors went off. Cryptex tried hard to bring the images back, but no use, all they had were the green code monitors. They brought Link to look at the codes and see if Trinity and Phoenix were fine, but it had been a long time since he worked with codes, and he couldn't interpret them so well.

Phoenix pushed Trinity away just in time to avoid her being shot by the Phantom, but he took the bullet in her arm instead. She fell on the ground in pain, while the Phantom was pointing his guns towards Trinity. Then something unusual happened. The Phantom looked Trinity in the eyes and dropped the gun. He seemed very confused. He grabbed his head in his hands and fell on his knees.

Trinity took out her gun and approached him. She pointed the gun against his chest, thinking she had the greatest opportunity to avenge Morpheus' death and the fact that he had tried so hard to kill her daughter.

"Die, you bastard!" she said, slowly pushing her fingers on the trigger.

But as Phoenix watched the scene she suddenly was brought back to the past, back on the alley where Morpheus was shot. She saw him struggle the Phantom, pulling his mask off, she could see his face… NO! THAT couldn't happen! It couldn't be HIM!

"Trinity stop!" she shouted as she jumped to deviate her gun from the Phantom.

"What are you doing? It's your chance to kill him!" Trinity told her.

"Take…his…mask…off…" she could barely say crying "his mask"

Trinity wasn't moving, pointing her gun at him again. Phoenix went and slowly removed his mask. The Phantom was not feeling well, he didn't oppose, it seemed he didn't even notice her.

"This is why I didn't let you shoot him!" Phoenix said revealing his face.

Trinity was shocked. In front of them, kneeling, stood no other but him, The One, the salvation of Zion… him… the man she loved… Thomas A. Anderson.

"Neo! You?" she said and wanted to go hug him.

"No! He's coming back to his senses, we must run. Let's go back to the Oracle, she MUST explain THIS" Phoenix said pulling Trinity away in the opposite direction.

TBC


	9. 9 Choices

_Before I begin I have to thank x.ShatteredImage.x for helping me with some fresh ideas that I used in Chapter 8 and that I'll be using in these last chapters as well!_

_**CHAPTER 9: CHOICES**_

On the neb everyone was worried because of the gunshot they heard. Link was trying to understand the codes on the monitor.

"I see Trinity and the other two codes I don't know"

Cryptex looked at the monitor.

"One of it is Phoenix, I know that for sure, but I don't know the third. I guess it's the Phantom" he said.

Link looked at the Phantom's code with more attention… It was a new code, but yet it looked very familiar in one way.

Niobe was watching over Neo.

"Boys, the monitors pick up some activity from Neo's brain" she told her sons.

For about five minutes the brain waves indicated that he was about to wake up, but then everything came back to the way it was.

The monitors began working again. They could all see Phoenix running, holding Trinity by her hand, like dragging her to follow her. Phoenix seemed hurt at the hand with which she was holding Trinity. Her face frowned with pain as she held her other hand on the wound to heal it.

They reached the Oracle's house and they lost the connection again. At least they knew they were fine.

And it was no time to worry for them, because the Sentinels attacked their ship and they had to head for Zion as quickly as possible.

Phoenix was exhausted by the time they entered the Oracle's house.

"Have a seat, my dear ones" the Oracle told them.

"What happened? Why him? It can't be him! What about the prophecy? How can I do what I have to do when he is who he is?" Phoenix shouted crying.

"Neo…killed…Morpheus? I…almost…shot…Neo" was all that Trinity could say.

"Calm down, I'll explain everything" the Oracle replied. "The Phantom is and is not Neo. Better said, the Phantom is Agent Smith."

"Smith? I thought Neo defeated him!" Trinity replied.

"You see, Neo didn't completely defeat Smith. By letting himself infected by him, he destroyed Smith's outer shell, but got his mind controlled by Smith. Inside Neo's head right now, there's a permanent battle between him and Smith. But Neo is too weak to gain control over himself. Smith did everything, he committed all those crimes, he killed Morpheus and Persephone. The worst thing is that Neo is aware of everything that Smith does. It was awful for Neo to see Morpheus get killed, to see that his mentor died believing that he was the killer. And as much as Neo would be happy to die and get rid of the burden of being controlled by Smith, Smith keeps him alive. They keep each other alive. Today when the Phantom looked into your eyes, Trinity, Neo got control over Smith, but it didn't last for long. It was the only time when he was about to break free, at the cost of his life, just for your love."

"Is there any way of helping Neo?" Phoenix asked.

"Yes, there is, and you know which is the way Phoenix" the Oracle replied, looking into the poor girl's eyes.

Phoenix saw in the Oracle's eyes the future, she saw what she had to do.

"Could you please tell me what are you talking about?" Trinity asked.

"All I can tell you, mother, is that Neo will be back" Phoenix said, giving Trinity a hug and crying "but I need you not to tell anyone about Neo and the Phantom! Do you promise?"

"If this brings my love back, I promise!" Trinity answered.

Everyone was relieved to see Trinity and Phoenix back on the Neb safe and sound.

"Phoenix! What happened, why do you both looked so sad?" Castor asked after giving her a kiss,

"We had a close encounter with the Phantom, we could barely escape him and we're a little frightened still" she answered.

"Why did you return to the Oracle's after that?" Castor insisted.

"She finally explained how I'll kill the Phantom and fulfill the prophecy" Phoenix answered with a bitter smile on her face. "But why are we back in Zion?"

"The war is getting worst, sentinels are attacking. In Zion we're safe for now" Castor replied with a sigh.

Neo had been left aboard Neb, connected to the monitors. Trinity decided to spend that night by his side, to watch upon him. But everything that happened that day was too much for her, and she fell asleep. She didn't see Phoenix sneak in and kiss Neo on the forehead, holding his hand, sobbing, then saying farewell to both of them…

Towards morning Trinity suddenly woke up… Was it a dream or did Neo's hand just move? She grabbed his hand. He squeezed it.

"Neo, do you hear me?" she asked "Neo?" She kissed him. Neo kissed her back, then he slowly opened his eyes, looking around him, very confused.

"Trinity! You're alive! And I woke up from my nightmare…" Neo said, giving Trinity another passionate kiss.

"It was not a nightmare, Neo" she sighed.

Neo was horrified.

"You mean everything was true? I did do all those things?" Neo hugged Trinity, crying. "Oh, Trin! Morpheus… and Persephone… and all those people… "

They were interrupted by Castor, who came running in.

"Trinity! I can't find Phoenix anywhere! Neo! You're awake!"

TBC


	10. 10 Another Mindless Crime

_**CHAPTER 10: ANOTHER MINDLESS CRIME…**_

"Morpheus!" Neo said on seeing Castor.

"No, Neo, that is one of Morpheus' twins, Castor." Trinity said before Neo could tell anything about Morpheus' death.

"Phoenix…" Neo said in a low voice, so that only Trinity could hear him. "I remember her, Smith tried to kill her several times"

"Neo, she is our daughter!" Trinity told him.

"Our daughter! He almost made me kill my own daughter too? Oh, Trin! What a nightmare! I wish I had died that night!" Neo answered, embracing Trinity and crying.

"Castor, have you looked for Phoenix all around Zion? She can't be anywhere else" Trinity addressed him.

"Yes, I did! Something must have happened to her!" Castor replied.

Pollux came running.

"I found this letter. Castor, you'd better read it at once!" he said in harsh voice.

Castor opened the letter and begun reading in a loud voice, to be heard by everyone.

"_Dear mortals, _

_Once again you prove me how stupid you mortals are! I didn't imagine that my plan will work out so great! Believing the story of a young girl with no memories and with super powers! Believing that getting out alive from an encounter with the Phantom is possible!_

_You make me laugh! _

_How I've had you fooled! Thinking that I was The One when I was your greatest enemy! You've lead me right to The One! Now that I know the Neb, that I know Zion and all of your week points, defeating you humans will be very easy!_

_It shall be a pleasure killing each and every one of you, watching you suffer and die, as I did with all of my victims, as I did with that stupid Morpheus, who tried he can resist me, which caused me all that trouble!_

_Prepare to meet your death today!_

_The Phantom (or should I say, Phoenix?)"_

Castor dropped the letter from his hand, tears began running down his check…How could that be? Phoenix was the Phantom? She had them fooled all along? That couldn't be! He loved her! He loved the one that killed his father?

"I'm going in to kill her" Pollux said. He got Cryptex on the neb, and got in the Matrix, in search of Phoenix.

Castor stood for about fifteen minutes without saying a word. Then he told Cryptex to get him in too, determined to stop his brother from hurting the woman she loved.

All this time, Neo and Trinity were too shocked to speak. What was it with that letter? Trinity knew that it couldn't be true since Neo had been the Phantom. But she wasn't allowed to tell that, Phoenix told her she would solve things, but what did she try to do?

"I know what she did!" Neo spoke. He close his eyes and began speaking: "Last night Phoenix wrote that letter…She was crying…Then she went into Castor's room…He was sleeping deeply, he didn't hear her…Phoenix kissed him and told him farewell…Then she came here, on the Neb…She kissed me on the forehead…Then she took my hand…" Neo frowned "And something happened…I suddenly got stronger, I got control over Smith, I got him weak, willing to leave me alone…" Neo sighed and continued "Phoenix slipped a note into your pocket, Trin, then she said farewell and got of the Neb. On her way out, she scratched herself with a nail on a finger…She kept her hand on the wound, but it kept bleeding…She told herself that it was just the way it had to be…She took a ship…she went to Machine City…She got connected into The Matrix and came to look for the Phantom, to look for me…She found the Phantom after some hours of searching, she found him agonizing on a dark lonely street…She addressed Smith, telling him that she was The One, that she had the powers of the Oracle and that by controlling her he could control all mankind…Smith agreed to let me go and infected her…Then I woke up…She let herself controlled by Smith to save me!" Neo finished, bursting into tears.

Trinity couldn't believe what Neo told her. She looked into her pocket and she found the note that Neo spoke about:

"_Dear Trinity and Neo, mom and dad,_

_Please forgive me for what I did! It was the only way to save Zion and save you, Neo! The only way I could think of! _

_Please, don't try to stop me! But you have to stop Castor from coming after me! Please!_

_Although we didn't get to spend much time together, I love you both! Don't suffer for me! Just forget me soon and live your love, you deserve to finally be together!_

_Phoenix"_

Trinity began crying, as well as Neo.

"She did it because of me! To save me! She will die for me! Oh! How cruel fate is! I wish I just died when Agent Smith first shot me! I wish I never took the red pill! I wish I never met you" Neo ended and lost his conscience.

Trinity couldn't believe what Neo said… He wished he had never met her? If he hadn't met her, maybe he wouldn't have taken the red pill… If she didn't kiss him back then, he would have remained dead… He couldn't have been serious! It must have been hard for him to live 25 years the way he lived, controlled by Smith, seeing all those people die, without being able to do anything…

Neo woke up soon, just in time to look up on the monitors and see what was going on in The Matrix.

He remembered Phoenix asked them to avoid castor getting in, so he told Cryptex to get him immediately. Trinity followed him.

Pollux had found Phoenix, she was dressed as the Phantom, but she didn't wear the mask.

"You came to meet your death so soon? You should have waited to die with the rest or humans, but well…" said Phoenix, pointing the gun in his direction.

"It is you who will die! You assassin!" Pollux answered, pointing his gun at Phoenix as well.

Phoenix suddenly began to let the gun down, she looked very confused.

Pollux aimed for her heart.

A gunshot was heart, and Pollux fell on his face.

Castor was standing behind him, still holding the gun I his direction, after having shot his brother in the back.

"Phoenix, my love are you fine? I didn't believe what you wrote, I came to take you back!" Castor said, with his eyes full of tears.

Phoenix seemed in real pain. When having given Neo her powers, she had kept for herself just enough to gain control over Smith. He didn't have any power over her, yet she chose to speak as she were Smith, to determine Castor to do what he had to do.

"Your love? You're as stupid as your father was! I have to thank you for making my work easier, though, by helping me get rid of Pollux! You did my dirty work this time! Now get ready to die, you fool! Die as your father did! It was such a pleasure to kill him! And it will be a pleasure to kill your mother too, and then to kill everyone you know and you love!"

Castor was crazed with pain. The letter was true, she had lied to him, she had made him kill his own brother! He pointed his gun at Phoenix and pulled the trigger. Once…twice…three times…he kept shooting until he ran out of bullets.

Phoenix fell breathless to the ground, She was dead, and along with her Smith was dead too. All of the the Sentinels deactivated themselves and stopped attacking Zion.

Trinity and Neo arrived, but it was too late. They walked up to Phoenix and took her in their arms, crying.

Castor watched them. He looked in his pocket and took out a bullet. He loaded the gun and pointed it against his head.

"Forgive me Phoenix, Neo, Trinity!" ha said and pulled the trigger. Castor fell down dead.

"The Prophecy is now fulfilled, the war is over" Neo sighed. "Another sacrifice done in the name of peace…" He began crying.

Trinity wanted to embrace him but he stepped behind.

"No! Our love was not meant to be! Now I understand everything! I was the One but the one was not supposed to get in love. Loving you caused this endless war! Everything is just my fault! What better sign that our love was forbidden than the death of our child? We can never be together! I must go, don't look for me!" he said and walked away.

Trinity was crying and ran after him, but she couldn't find him, he had got out. She got out, but Neo wasn't on the Neb any more.

"Cryptex, where is Neo?" Trinity desperately asked.

"He left without saying anything" he replied.

Trinity got out of the ship, back into Zion.

The machines were getting deactivated. The artificial Matrix was beginning to fade away.

The sky got clear. Everyone got out of Zion to see the first sunrise in their life, the first real sunrise.

Trinity watched the clear sky, remembering what she had seen 25 years before, before crashing. She looked in front of her and saw Neo watching the sunrise too. Then he walked away from Zion. It was the last time she ever saw him…

THE END


End file.
